Crystal structures of Lys‐63‐linked tri‐ and di‐ubiquitin reveal a highly extended chain architecture

Abstract

The covalent attachment of different types of poly-ubiquitin chains signal different outcomes for the proteins so targeted. For example, a protein modified with Lys-48-linked poly-ubiquitin chains is targeted for proteasomal degradation, whereas Lys-63-linked chains encode non-degradative signals. The structural features that enable these different types of chains to encode different signals have not yet been fully elucidated. We report here the X-ray crystal structures of Lys-63-linked tri- and di-ubiquitin at resolutions of 2.3 and 1.9 Å, respectively. The tri- and di-ubiquitin species adopt essentially identical structures. In both instances the ubiquitin chain assumes a highly extended conformation with a left-handed helical twist; the helical chain contains four ubiquitin monomers per turn and has a repeat length of approximately 110 Å. Interestingly, Lys-48 ubiquitin chains also adopt a left-handed helical structure with a similar repeat length. However, the Lys-63 architecture is much more open than that of Lys-48 chains and exposes much more of the ubiquitin surface for potential recognition events. These new crystal structures are consistent with the results of solution studies of Lys-63 chain conformation, and reveal the structural basis for differential recognition of Lys-63 versus Lys-48 chains.

Three-Dimensional Architecture of the Human BRCA1-A Histone Deubiquitinase Core Complex

“…Modeling of the path of the bound Ub substrate (Figure 3B) shows that, beyond the Ub pair bound at the BRCC36 active site, additional interactions with the core assembly are likely to occur between the UEV domains of BRCC45 and ubiquitin units on the side of the chain that is ultimately linked to the modified nucleosome. Unlike K48-linked Ub, which shows substantial and conformationally restrictive Ub-Ub interactions, K63-linked Ub chains are considerably more flexible (Komander et al., 2009b, Weeks et al., 2009). While Ub interactions with either of the two symmetrically arranged BRCC36 components in the 2×4 assembly is feasible, closer inspection of our modeled Ub complex (Figure 3B) suggests the intriguing possibility that BRCC45 tethers the ubiquitin chain substrate being processed by the opposing BRCC36 subunit in the 2×4 complex.…”

Ubiquitin enzymes in the regulation of immune responses

“…2009, Weeks et al. 2009). These different three-dimensional conformations of ubiquitin chains that depend on the linkage types result in a variety of different functional outcomes (discussed in more detail in section Recognition of ubiquitin by ubiquitin binding domains (UBDs)).…”

Enhancing ubiquitin crystallization through surface-entropy reduction

“…The A chain from PDB entry 3h7p (Weeks et al, 2009) was used as the probe molecule for molecular replacement. Refinement was carried out using PHENIX v.1.8.2-1309 (Adams et al, 2010).…”